Article
Marine & Freshwater Biology
Xinghai Zhu, Ping Ni, Marc Sturrock, Yangfan Wang, Jun Ding, Yaqing Chang, Jingjie Hu, Zhenmin Bao
Summary: In this study, the genetic basis for papilla number diversity in sea cucumbers was investigated using genome-wide association studies. Two significant SNPs associated with papilla number were identified, along with potential candidate genes related to papilla formation and cellular activity. These findings provide valuable information for selective breeding in sea cucumbers.
MARINE LIFE SCIENCE & TECHNOLOGY
(2022)
Article
Biology
Wei Cui, Da Huo, Shilin Liu, Lili Xing, Fang Su, Hongsheng Yang, Lina Sun
Summary: This study constructed a high-density genetic linkage map for sea cucumbers and identified an important candidate gene related to growth traits. The results provide valuable insights for genetically improving the growth traits of sea cucumbers.
Article
Biodiversity Conservation
Viktoriia D. Yagodina, Evgeniia Bondar, Vladimir A. Brykov
Summary: The genetic diversity and population structure of the sea cucumber Apostichopus japonicus in Peter the Great Gulf, Sea of Japan, were studied. It was found that the population showed high heterogeneity and heterozygote deficiency.
MARINE BIODIVERSITY
(2022)
Article
Plant Sciences
Yuan-yuan Zhang, Hong-kun Li, Xiao Huang, Yu-jiao Yuan, Xiao-fei Zhang, Xin-sheng Gao, Xiang-jun Wang, Ming-ming Wei, Hua-sun Huang, Weiguo Li
Summary: This study evaluates the MHR of 2n female gametes of rubber tree clone GT1, confirming their derivation from SDR and providing insights into the centromere location. These findings are important for understanding the mechanism of 2n gametogenesis and developing related markers.
PLANT REPRODUCTION
(2023)
Article
Marine & Freshwater Biology
V. D. Yagodina, N. M. Batishcheva, V. A. Brykov
Summary: The genetic diversity of Apostichopus japonicus in Peter the Great Bay was assessed using five microsatellite markers. The study revealed polymorphism in all loci and a deficiency of heterozygotes, resulting in an average inbreeding coefficient greater than zero. Additionally, null alleles were detected at some microsatellite loci, leading to a decrease in observed heterozygosity and deviations from the Hardy-Weinberg equilibrium.
RUSSIAN JOURNAL OF MARINE BIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Junhong Zheng, Hongtao Nie, Xiwu Yan
Summary: In this study, gene expression of two shell colors in Meretrix petechialis was analyzed using sequence-related amplified polymorphism-cDNA to identify associated molecular markers. Through validation experiments, four markers were confirmed to be related to shell color in M. petechialis, providing a theoretical basis for further research on shell color regulation.
ANIMAL BIOTECHNOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Hongtao Nie, Kunyin Jiang, Ning Li, Kifat Jahan, Liwen Jiang, Zhongming Huo, Xiwu Yan
Summary: This study investigated the relationship between shell color and gene expression in the Manila clam through transcriptomic sequencing and real-time qPCR analysis, revealing the significant role of melanin synthesis in shell pigmentation and its close association with surface pattern formation. The discovery of the porphyrin metabolism combined with tyrosinase and melanogenesis signaling pathway as a novel mechanism in shell color determination of Ruditapes philippinarum sheds light on the pigmentation and coloration process in this species.
ANIMAL BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Weiming Teng, Xi Xie, Hongtao Nie, Yamin Sun, Xiangfeng Liu, Zuoan Yu, Jie Zheng, Hongyue Liu, Dacheng Li, Ming Zhang, Zhisong Wang, Shouwei Zhu, Shangkun Du, Shaojun Du, Qi Li, Qingzhi Wang
Summary: This study reported a high-quality chromosome-level genome assembly of Scapharca kagoshimensis, aimed at unraveling the molecular basis of heme biosynthesis and developing genomic resources for genetic breeding and population genetics in ark shells. The assembly represents 93.4% completeness and contains a total of 24,908 protein-coding genes, with enrichment analyses indicating expansion of genes in heme biosynthesis pathways and positive selection of haemoglobin genes in the genome of S. kagoshimensis, providing important insights into the molecular mechanisms and evolution of heme biosynthesis in mollusks. This valuable genome assembly will serve as a foundation for investigating the diverse biological functions and evolutionary adaptations of S. kagoshimensis.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Fisheries
Shasha Dong, Chensi Wang, Hongtao Nie, Zhihui Yin, Yanming Zhang, Kunyin Jiang, Zhongming Huo, Xiwu Yan
Summary: This study investigated the function of ISP II in the cold tolerance and resistance of Ruditapes philippinarum. The results showed that ISP II had a potential antifreeze effect and could improve the cold resistance of R. philippinarum. The findings provide molecular insights for improving the low-temperature resistance and immunity of shellfish.
Article
Fisheries
Kifat Jahan, Hongtao Nie, Zhihui Yin, Yanming Zhang, Ning Li, Xiwu Yan
Summary: Increasing temperature causes rapid changes in oceanic environments, and understanding the responses of marine animals to these changes is crucial for predicting future biodiversity loss or gain. In this study, the molecular mechanisms of adaptation to acute temperature change in low and high latitude populations of the Manila clam were investigated. Transcriptome analysis revealed temperature-responsive genes and pathways involved in the adaptation of clams to temperature stress. Differences in the response and adaptation mechanisms between the two clam populations were found, providing valuable information for improving temperature stress resistance in aquaculture and predicting future biodiversity trends.
Article
Biotechnology & Applied Microbiology
Qiaoyue Xu, Hongtao Nie, Zhihui Yin, Yanming Zhang, Zhongming Huo, Xiwu Yan
Summary: The study revealed that shell color formation and regulation in the Manila clam is negatively regulated by multiple miRNAs, which may affect melanin formation and participate in the calcium signaling pathway. Verification of candidate miRNAs and target genes in different shell color groups suggested that miR-7, miR-71, and miR-133 may play important roles in shell color pigmentation.
MARINE BIOTECHNOLOGY
(2021)
Article
Evolutionary Biology
Tao Xu, Lu Qi, Lingfeng Kong, Qi Li
Summary: This study sequenced 10 new mitochondrial genomes and analyzed them with previously published nine mitogenomes and six transcriptomic data representing six families of Patellogastropoda. Based on amino acid sequences of 13 protein-coding genes, a well-supported phylogeny was reconstructed, revealing Lottioidea as non-monophyletic with two well-supported lineages. Comparison of gene order among families, genera and species showed that Nacellidae has a conserved gene arrangement, while Lottiidae exhibits extensive rearrangements.
Article
Fisheries
Xiangfeng Liu, Xi Xie, Hongyue Liu, Hongtao Nie, Haitao Ma, Dacheng Li, Weiming Teng, Hualin Li, Zuoan Yu, Yongxin Sun, Yun Zhang, Ming Zhang, Qingzhi Wang
Summary: The combination of population genetics and genomic data has enhanced scientists' ability to make ecological inferences in wild populations, allowing for the detection of previously unidentified structures and more accurate demographic parameter estimates. A study on the ark shell populations from China, Korea, and North Korea revealed a significant genetic divergence among Chinese populations, highlighting the importance of properly managing individual translocations to preserve genetic diversity.
AQUACULTURE REPORTS
(2022)
Article
Genetics & Heredity
Tao Xu, Lingfeng Kong, Qi Li
Summary: Recently, species identification has advanced from DNA barcoding to genome skimming based on shotgun sequencing. Genome skimming has been primarily used for assembling organelle genomes, while discarding most of the nuclear genome. A new approach using unassembled genome skims has been proposed for sample identification, which effectively improves phylogenetic signal and identification resolution. Skmer and APPLES have been shown to work well in estimating genomic distance and performing phylogenetic placement using low-coverage genome skims of birds and insects. In this study, Skmer and APPLES were used to perform assembly-free and alignment-free species identification and phylogenetic placement of 11 patellogastropods. Skmer selects the best matching or closest species with COI barcodes, except for species belonging to the same family as the query, under different sizes of genome skims, regardless of whether the data corresponding to the query species are present in the reference database. When the reference database is sparse, APPLES cannot accurately place patellogastropods in the correct phylogenetic position. This study demonstrates the feasibility of genome skims for patellogastropod species identification and highlights the need for establishing a database to share genome skims.
Article
Genetics & Heredity
Yijing Zhu, Qi Li, Hong Yu, Shikai Liu, Lingfeng Kong
Summary: This research identified two tyrosinase-like protein genes in the Pacific oyster and found that they were dominantly expressed in the mantle, especially in the edge mantle. These genes were mainly found in oysters with black shells and showed positive signals in the outer epithelium of the outer fold. Knockdown of these genes significantly reduced the mRNA expression levels and the tyrosinase activity in the mantle, as well as decreased the number of melanosomes. These findings suggest that these genes may be involved in melanin synthesis and provide insight into the regulation mechanism of shell pigmentation in the Pacific oyster.
Article
Evolutionary Biology
Lu Qi, Biyang Xu, Lingfeng Kong, Qi Li
Summary: Neritidae is a species-rich family with controversial classification, particularly regarding the taxonomic position of Smaragdiinae. Through sequencing mitochondrial genomes and reassembling transcriptome data, we reconstructed the phylogeny of Neritidae with 23 species and found two monophyletic groups, Neritinae and Neritininae, with Smaragdia rangiana nested within Neritininae. The monophyly of Clithon and Neritina was not recovered, and the most recent common ancestor of Neritidae had a smooth shell.
Article
Genetics & Heredity
Bingyu Guo, Lingfeng Kong
Summary: In the context of diminishing global biodiversity, this study examines the validity and practicality of species delimitation methods for identifying neglected and undescribed biodiverse species. The results suggest that distance-based methods are generally superior to tree-based methods, with the ASAP method being the most efficient. In terms of phylogenetic methods, the single threshold version of GMYC performs better and PTP shows higher efficiency in delimiting species. Additionally, GMYC is significantly influenced by taxonomic rank, performing poorly at the genus level.
Article
Engineering, Marine
Yiming Hu, Qi Li, Chengxun Xu, Shikai Liu, Lingfeng Kong, Hong Yu
Summary: This study investigated the differences in temperature and salinity tolerance between C. nippona and C. gigas spat and determined the optimal environmental conditions for the aquaculture of C. nippona spat. The results showed that C. nippona had lower survival rates than C. gigas under temperature changes and salinity decreases, but higher survival rates with increasing salinity. The findings suggest that particular attention should be paid to the inferior adaptability of C. nippona when farming outside their natural habitats.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2023)
Article
Evolutionary Biology
Yi Yu, Lingfeng Kong, Qi Li
Summary: In this study, the sequencing of 11 muricid mitochondrial genomes revealed the conservation of gene arrangement, genome size, and nucleotide composition within the family. Phylogenetic analysis supported the monophyly of each subfamily and redefined the relationships between subfamilies and genera. These findings provide new insights into the classification and evolutionary history of Muricidae.
Article
Biodiversity Conservation
Lu Qi, Biyang Xu, Lingfeng Kong, Qi Li
Summary: This study conducted a survey of micromolluscs in the intertidal zone of the Yellow Sea and Bohai Sea, revealing the diversity of sedimentary environments and molluscs in this area. It found that the current research on micromolluscs is seriously underestimated. A total of 20 species were described, belonging to 16 families, four orders, and two classes. The collection, preservation, and preparation methods of morphological characteristic structures by scanning electron microscopy (SEM) were explored.
BIODIVERSITY DATA JOURNAL
(2023)
Article
Fisheries
Hunter S. Bailey, Ashley N. Fincannon, Lee A. Fuiman
Summary: This study investigated the transfer of fatty acids from broodstock diets to eggs and the time needed for the eggs to equilibrate to the diet in Southern flounder. The findings indicate that different diet treatments significantly affect the fatty acid composition of eggs, and it takes 8-16 weeks for the eggs to adapt to changes in the adult diet. These results are important for improving broodstock diets and feeding protocols in stock-enhancement programs.
Article
Fisheries
Yu Liu, Mingtao Lei, Hector Victor, Yan Wang
Summary: This study confirms the feasibility of replacing raw fish diet with a formulated diet in commercial farming of large yellow croaker, which can increase fish survival and yield, and reduce feed cost and body lipid deposition.
Article
Fisheries
Xiaoyan Zhang, Lize San, Yucong Yang, Yuehong Tao, Jiangong Ren, Yufeng Liu, Zhongwei He, Jiashuo Di, Ziteng Pei, Guixing Wang, Jilun Hou
Summary: Gynogenesis is an effective technique for establishing homogeneous lines and confirming potential chromosomal mechanisms of sex determination in fish. This study successfully induced gynogenetic families in Thamnaconus modestus and established a complete method for gynogenesis induction.
Article
Fisheries
Julieta C. Martinelli, Megan Considine, Helen R. Casendino, Carolyn M. Tarpey, Isadora Jimenez-Hidalgo, Jacqueline L. Padilla-Gamino, Teri L. King, Lorenz Hauser, Steven Rumrill, Chelsea L. Wood
Summary: Shell-boring polychaetes have caused significant damage to mariculture operations worldwide, particularly in the US Pacific region. This study provides a comprehensive dataset on the prevalence, species distribution, and environmental associations of these parasites, highlighting the impact of season, culturing methods, and environmental factors on infestation.
Article
Fisheries
Juan Gao, Xueshan Li, Kangle Lu, Kai Song, Jian Zhang, Ling Wang, Chunxiao Zhang
Summary: This study investigated the effects of dietary protein levels on growth performance, antioxidant capacity, digestive enzyme activity, and metamorphosis rate of bullfrog tadpoles. The optimal dietary protein level for bullfrog tadpoles was estimated to be 42.49%-46.50% of the diet.
Article
Fisheries
Qiang Li, Lijun Duan, Dongsheng Jin, Yuxin Chen, Yirong Lou, Qianjin Zhou, Zhongjie Xu, Fangjie Chen, Hongxian Chen, Guizong Xu, Maocang Yan, Guanjun Yang, Jianfei Lu, Yanjun Zhang, Jiong Chen
Summary: This study developed a centrifugal microfluidic chip with on-chip RPA to detect five pathogenic microorganisms. The chip enabled the parallel analysis of six genetic markers from a single sample and allowed for the highly automated detection of multiple samples. Compared with PCR and DNA sequencing, the on-chip RPA assay showed high sensitivity and specificity for detecting multiple pathogens in shrimp aquaculture.
Article
Fisheries
Xingchen Huo, Pengxu Wang, Fengxia Zhao, Qian Liu, Qingqing Tian, Lingjie Tang, Maolin Lv, Zhaohui Wei, Chunrong Yang, Jianguo Su
Summary: Bacterial diseases in aquaculture ponds have negative effects on sustainable development. The use of composite I20 biotherapy has been shown to effectively treat bacterial diseases in bullfrog ponds, providing a new strategy for controlling bacterial diseases in aquaculture.
Article
Fisheries
Peng Yin, Takaya Saito, Per Gunnar Fjelldal, Bjorn Tharandur Bjornsson, Sofie Charlotte Remo, Sandeep Sharma, Rolf Erik Olsen, Kristin Hamre
Summary: This study aims to investigate the effect of seasonal changes in temperature and photoperiod on the redox metabolism of Atlantic salmon at the molecular level. The research findings suggest that the changing photoperiod and temperature influenced the redox metabolism of Atlantic salmon, highlighting the importance of oxidative status in the ecological implications.
Article
Fisheries
Nicholas Oppong Mensah, Jeffery Kofi Asare, Emmanuel Tetteh-Doku Mensah, Ernest Christlieb Amrago, Frank Osei Tutu, Anthony Donkor
Summary: This study investigates aquaculture farmers' preference for climate-smart aquaculture insurance products, the challenges they face, and their preferred insurance coverage. The results show that farmers prefer Climate-Induced Aquaculture Stock Mortality Insurance and the most significant constraint is the delay in claim settlement.
Article
Fisheries
Qiu-Ping Chai, Pei Wu, Wei-Dan Jiang, Yang Liu, Hong-Mei Ren, Xiao-Wan Jin, Lin Feng, Xiao-Qiu Zhou
Summary: The study found that appropriate levels of potassium diformate (KDF) can enhance the immune defense and mediate the inflammatory process in fish, possibly through the regulation of T cell differentiation via JAK-STAT and NF-kappa B signaling pathways.
Article
Fisheries
Tian Zhu, Haomin Jia, Haopeng Zhang, Yujing Xiao, Cui Han, Jiaxin Yang
Summary: Chicken manure has significant effects on the cultivation of Chlorella and rotifers. The optimal amount of chicken manure extract for continuous cultivation is 10 mLL-1. Chicken manure can promote the growth of Chlorella and improve the fatty acid composition, indirectly enhancing the growth condition and fatty acid content of rotifers.
Article
Fisheries
Zheng Luo, Yang Yu, Zhenning Bao, Fuhua Li
Summary: This study analyzed the heritability and genetic correlation of two growth traits in Pacific white shrimp and evaluated the genomic prediction using different genomic selection models. The results showed that the NeuralNet model had the highest prediction accuracy and better prospects for predicting shrimp growth traits.
Article
Fisheries
Alberto Ruiz, Ignasi Sanahuja, Karl B. Andree, Dolors Furones, Paul G. Holhorea, Josep A. Calduch-Giner, Jose J. Pastor, Marc Vinas, Jaume Perez-Sanchez, Sofia Morais, Enric Gisbert
Summary: Supplementing diets with a combination of spice oleoresins can reduce lipid accumulation and inflammation in farmed fish. The combination of spice oleoresins also has an immunomodulatory effect on the fish's intestinal immune system, potentially offering anti-inflammatory benefits.
Article
Fisheries
Beibei Zhao, Renhui Mei, Le Li, Di Hu, Lei Li
Summary: This study reveals that JfCXCL8_L1a and JfCXCL8_L1b have different immune pathways, and JfCXCL8_L1b plays a significant role in enhancing the adaptive immunity of T cell-dependent antigen.
Article
Fisheries
Yuhang Liu, Danying Cao, Nan Wu, Xuyang Zhao, Qingsong Zhu, Lian Su, Fatima Altaf, Qianqian Zhang, Haokun Liu, Yongming Li, Bruno Hamish Unger, Yingyin Cheng, Wanting Zhang, Aihua Li, Yaping Wang, Xiao-Qin Xia
Summary: Based on previous research, sinomenine has been found to protect mucosal immunity in farmed fish species by preventing intestinal pathological changes and regulating gene expression related to inflammation. It also enhances immune homeostasis and controls the growth of pathogenic bacteria.
